Alexander Goesmann

Summary

Affiliation: University of Bielefeld
Country: Germany

Publications

  1. ncbi request reprint PathFinder: reconstruction and dynamic visualization of metabolic pathways
    Alexander Goesmann
    Center for Genome Research, Department of Genetics, Bielefeld University, 33594 Bielefeld, Germany
    Bioinformatics 18:124-9. 2002
  2. ncbi request reprint Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology
    Alexander Goesmann
    Center for Genome Research, Bielefeld University, D 33594 Bielefeld, Germany
    J Biotechnol 106:157-67. 2003
  3. doi request reprint Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor
    Lutz Krause
    Centrum für Biotechnologie CeBiTec, Universitat Bielefeld, D 33594 Bielefeld, Germany
    J Biotechnol 136:91-101. 2008
  4. doi request reprint Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant
    Andreas Schluter
    Department of Genetics, Bielefeld University, Postfach 100131, D 33501 Bielefeld, Germany
    J Biotechnol 136:65-76. 2008
  5. ncbi request reprint EMMA: a platform for consistent storage and efficient analysis of microarray data
    Michael Dondrup
    Center for Genome Research, Bielefeld University, D 33594 Bielefeld, Germany
    J Biotechnol 106:135-46. 2003
  6. pmc Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
    Heiko Neuweger
    Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
    BMC Syst Biol 3:82. 2009
  7. ncbi request reprint Bioinformatics support for high-throughput proteomics
    Andreas Wilke
    Center for Genome Research, Bielefeld University, D 33594 Bielefeld, Germany
    J Biotechnol 106:147-56. 2003
  8. pmc EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data
    Michael Dondrup
    Computational Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany
    BMC Bioinformatics 10:50. 2009
  9. ncbi request reprint Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique
    Olaf Kaiser
    Lehrstuhl fur Genetik, Universitat Bielefeld, D 33594 Bielefeld, Germany
    J Biotechnol 106:121-33. 2003
  10. pmc TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    Naryttza N Diaz
    Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
    BMC Bioinformatics 10:56. 2009

Detail Information

Publications67

  1. ncbi request reprint PathFinder: reconstruction and dynamic visualization of metabolic pathways
    Alexander Goesmann
    Center for Genome Research, Department of Genetics, Bielefeld University, 33594 Bielefeld, Germany
    Bioinformatics 18:124-9. 2002
    ..To utilize automated genome analysis on the level of metabolic pathways new methods for the dynamic representation and visualization of pathways are needed...
  2. ncbi request reprint Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology
    Alexander Goesmann
    Center for Genome Research, Bielefeld University, D 33594 Bielefeld, Germany
    J Biotechnol 106:157-67. 2003
    ..We have implemented a Bioinformatics Resource for the Integration of heterogeneous Data from Genomic Explorations (BRIDGE) and illustrate the usability of our approach as a platform for systems biology for two sample applications...
  3. doi request reprint Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor
    Lutz Krause
    Centrum für Biotechnologie CeBiTec, Universitat Bielefeld, D 33594 Bielefeld, Germany
    J Biotechnol 136:91-101. 2008
    ..Finally, the results unveiled that most of the organisms constituting the sample are still unexplored...
  4. doi request reprint Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant
    Andreas Schluter
    Department of Genetics, Bielefeld University, Postfach 100131, D 33501 Bielefeld, Germany
    J Biotechnol 136:65-76. 2008
    ..EGT analysis thus proofed to be a very valuable method to explore genetic diversity and composition of the present plasmid metagenome dataset...
  5. ncbi request reprint EMMA: a platform for consistent storage and efficient analysis of microarray data
    Michael Dondrup
    Center for Genome Research, Bielefeld University, D 33594 Bielefeld, Germany
    J Biotechnol 106:135-46. 2003
    ..In addition to routine data analysis algorithms, the system can be integrated with other components that contain additional data sources (e.g. genome annotation systems)...
  6. pmc Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
    Heiko Neuweger
    Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
    BMC Syst Biol 3:82. 2009
    ..It has become obvious that the application of web-based and user driven software tools has great potential and benefits from the use of open and standardized formats for the description of pathways...
  7. ncbi request reprint Bioinformatics support for high-throughput proteomics
    Andreas Wilke
    Center for Genome Research, Bielefeld University, D 33594 Bielefeld, Germany
    J Biotechnol 106:147-56. 2003
    ..First tests showed that the automation resulted in a significant saving of time. Furthermore, the quality and interpretability of the results was improved in all cases...
  8. pmc EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data
    Michael Dondrup
    Computational Genomics, Center for Biotechnology, Bielefeld University, 33594 Bielefeld, Germany
    BMC Bioinformatics 10:50. 2009
    ..Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems...
  9. ncbi request reprint Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique
    Olaf Kaiser
    Lehrstuhl fur Genetik, Universitat Bielefeld, D 33594 Bielefeld, Germany
    J Biotechnol 106:121-33. 2003
    ..vesicatoria 85-10. Our pipeline relies on standard tools (e.g. PHRED/PHRAP, CAP3 and Consed/Autofinish) wherever possible, supplementing them with new tools (BioMake and BACCardI) to achieve the aims described above...
  10. pmc TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    Naryttza N Diaz
    Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
    BMC Bioinformatics 10:56. 2009
    ..We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning...
  11. doi request reprint Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
    Jochen Blom
    Computational Genomics, Bielefeld University, Bielefeld, Germany
    Bioinformatics 27:1351-8. 2011
    ..Furthermore, most approaches return only one best hit for every query sequence, thus losing the potentially valuable information of alternative alignment positions with identical scores...
  12. doi request reprint Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments
    Stefan P Albaum
    Computational Genomics, Center for Biotechnology CeBiTec, Biodata Mining and Applied Neuroinformatics Group, Faculty of Technology, Bielefeld University, Bielefeld, Germany
    Bioinformatics 25:3128-34. 2009
    ....
  13. doi request reprint The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome
    Susanne Schneiker-Bekel
    Center for Biotechnology CeBiTec, Bielefeld University, Institute for Genome Research and Systems Biology, Universitatsstr 27, D 33615 Bielefeld, Germany
    J Biotechnol 155:20-33. 2011
    ..Most remarkably, pSmeSM11b contains a new gene cluster predicted to be involved in polysaccharide biosynthesis. Compilation of the S. meliloti SM11 genome sequence contributes to an extension of the S. meliloti pan-genome...
  14. pmc EDGAR: a software framework for the comparative analysis of prokaryotic genomes
    Jochen Blom
    Computational Genomics, Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
    BMC Bioinformatics 10:154. 2009
    ..A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons...
  15. pmc TRUNCATULIX--a data warehouse for the legume community
    Kolja Henckel
    Bioinformatics Resource Facility, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
    BMC Plant Biol 9:19. 2009
    ..Thus, we created the data warehouse TRUNCATULIX, an integrative database of Medicago truncatula sequence and expression data...
  16. pmc Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing
    Sebastian Jaenicke
    Computational Genomics, Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
    PLoS ONE 6:e14519. 2011
    ....
  17. doi request reprint MeltDB: a software platform for the analysis and integration of metabolomics experiment data
    Heiko Neuweger
    International NRW Graduate School in Bioinformatics and Genome Research, Bielefeld University, Germany
    Bioinformatics 24:2726-32. 2008
    ..Currently there exists no such system that on the one hand supports preprocessing of raw datasets but also allows to visualize and integrate the results of higher level statistical analyses within a functional genomics context...
  18. doi request reprint Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing
    Martha Zakrzewski
    Computational Genomics, Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
    J Biotechnol 158:248-58. 2012
    ..In the future, key transcripts for the biogas production process will provide valuable markers for evaluation of the performance of biogas-producing microbial communities with the objective to optimize the biotechnology of this process...
  19. doi request reprint Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities
    Jessica Schneider
    Center for Biotechnology, Bielefeld University, Bielefeld, Germany
    FEMS Yeast Res 12:382-6. 2012
    ..anomalus DSM 6766 coding for proteins participating in antimicrobial activities...
  20. pmc GenDB--an open source genome annotation system for prokaryote genomes
    Folker Meyer
    Center for Genome Research, Department of Biology, Bielefeld University, Bielefeld, Germany
    Nucleic Acids Res 31:2187-95. 2003
    ..In addition to its use as a production genome annotation system, it can be employed as a flexible framework for the large-scale evaluation of different annotation strategies. The system is open source...
  21. ncbi request reprint Development of joint application strategies for two microbial gene finders
    Alice C McHardy
    Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
    Bioinformatics 20:1622-31. 2004
    ..Due to the faster pace and increasing number of genome projects currently underway, it is becoming especially important to have performant methods for this task...
  22. doi request reprint RAPYD--rapid annotation platform for yeast data
    Jessica Schneider
    Computational Genomics, Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
    J Biotechnol 155:118-26. 2011
    ..An in-depth application example of the yeast Meyerozyma guilliermondii illustrates the functionality of RAPYD. A user-friendly web interface is available at https://rapyd.cebitec.uni-bielefeld.de...
  23. doi request reprint Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology
    Rafael Szczepanowski
    Department of Genetics, Bielefeld University, Postfach 100131, D 33501 Bielefeld, Germany
    J Biotechnol 136:54-64. 2008
    ..Plasmid metagenome sequence reads could be assembled into 605 contigs with a minimum length of 500 bases. Contigs predominantly encode plasmid survival functions and transposition enzymes...
  24. doi request reprint The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology
    Andreas Schluter
    Lehrstuhl fur Genetik, Universitat Bielefeld, D 33594 Bielefeld, Germany
    J Biotechnol 136:77-90. 2008
    ..Metagenome sequence data from a biogas-producing microbial community residing in a fermenter of a biogas plant provide the basis for a rational approach to improve the biotechnological process of biogas production...
  25. doi request reprint MetaSAMS-A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets
    Martha Zakrzewski
    Institute for Bioinformatics IfB, Center for Biotechnology CeBiTec, Bielefeld University, Bielefeld, Germany
    J Biotechnol 167:156-65. 2013
    ..The MetaSAMS web interface is available at https://metasams.cebitec.uni-bielefeld.de. ..
  26. pmc Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10
    Jessica Schneider
    Institute for Genome Research and Systems Biology, Bielefeld University, Bielefeld, Germany
    Eukaryot Cell 11:1582-3. 2012
    ..This information will contribute to the metabolic engineering of this yeast to improve the yield and spectrum of acetylated sphingoid bases in biotechnological production...
  27. pmc WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
    Wolfgang Gerlach
    Faculty of Technology, Bielefeld University, Bielefeld, Germany
    BMC Bioinformatics 10:430. 2009
    ..CARMA is a new software pipeline for the characterisation of species composition and the genetic potential of microbial samples using short, unassembled reads...
  28. pmc CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data
    Heiko Neuweger
    Computational Methods for Emerging Technologies group, Bielefeld University, Bielefeld, Germany
    BMC Syst Biol 1:55. 2007
    ..The discovery of transcriptional regulatory interactions has become a major topic in modern functional genomics...
  29. doi request reprint Conveyor: a workflow engine for bioinformatic analyses
    Burkhard Linke
    Bioinformatics Resource Faciliy, Center for Biotechnology and Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
    Bioinformatics 27:903-11. 2011
    ..The currently available workflow systems achieve this goal, but fundamentally differ in their way of executing workflows...
  30. doi request reprint Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid
    Daniel Wibberg
    Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D 33501 Bielefeld, Germany
    J Biotechnol 155:50-62. 2011
    ..6 Mb) is only distantly related to the plasmid pAtC58 of A. tumefaciens C58 and shows a mosaic structure. A tumor-inducing Ti-plasmid is missing in the sequenced strain H13-3 indicating that it is a non-virulent isolate...
  31. pmc Phylogenetic classification of short environmental DNA fragments
    Lutz Krause
    Center for Biotechnology CeBiTec, Bioinformatics Resource Facility BRF, Bielefeld University, D 33594 Bielefeld, Germany
    Nucleic Acids Res 36:2230-9. 2008
    ..The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed...
  32. doi request reprint Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing
    Jennifer Becker
    Centrum für Biotechnologie, Universitat Bielefeld, 33594 Bielefeld, Germany
    J Biotechnol 156:227-35. 2011
    ..The present manuscript represents a data set of assembled and annotated genes for CHO cells that can now be used for a detailed analysis of the molecular functioning of CHO cell lines...
  33. doi request reprint Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14
    Daniel Wibberg
    Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D 33501 Bielefeld, Germany CLIB Graduate Cluster Industrial Biotechnology, CeBiTec, Bielefeld University, D 33501 Bielefeld, Germany
    J Biotechnol 167:142-55. 2013
    ..The average number of exons per gene is five. Exons have a mean length of 214bp, whereas introns on average are 66bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories. ..
  34. doi request reprint The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis
    Joël F Pothier
    Agroscope Changins Wädenswil ACW, Plant Protection Division, Wädenswil, SwitzerlandCeBiTec, Bielefeld University, Bielefeld, Germany
    FEMS Microbiol Lett 323:52-60. 2011
    ..This plasmid was not detected in any other X. arboricola pathovars (n=12), indicating the potential for the application of the pXap41 PCR method as a pathovar-level detection and identification tool...
  35. ncbi request reprint Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses
    Helge Küster
    Institute for Genome Research, Center for Biotechnology CeBiTec, Universitat Bielefeld, Universitatsstrasse 25, 33594 Bielefeld, Germany
    Phytochemistry 68:19-32. 2007
    ..Together, the EST- and transcriptome databases can be mined to identify candidate genes for targeted functional studies...
  36. pmc Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms
    Sebastian Oehm
    Center for Biotechnology CeBiTec, Bielefeld University, D 33594 Bielefeld, Germany
    Nucleic Acids Res 36:W433-7. 2008
    ..Additionally, users can upload their own annotation data. This website is free and open to all users and there is no login requirement. It is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/cpa/index.html...
  37. ncbi request reprint The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies
    Thomas Bekel
    Computational Genomics, Center for Biotechnology CeBiTec, Universitat Bielefeld, Bielefeld, Germany
    J Biotechnol 140:3-12. 2009
    ..The system has been implemented to cope with several thousands of sequences, efficiently processing them and storing the results for further analysis. With the project setup, SAMS automatically recognizes the data type...
  38. pmc Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format
    Justina Krawczyk
    Computational Genomics, Center for Biotechnology CeBiTec, 33594 Bielefeld, Germany
    Source Code Biol Med 4:4. 2009
    ..To allow for a quick conversion of the proprietary data format into a commonly used one, toolkits are required that reach this aim and can be easily integrated into workflow systems...
  39. pmc The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence
    Eva Trost
    Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universitat Bielefeld, Bielefeld, Germany
    BMC Genomics 11:728. 2010
    ..To detect potential virulence factors and corresponding gene-regulatory networks in this human isolate, the genome sequence of C. pseudotuberculosis FCR41 was determined by pyrosequencing and functionally annotated...
  40. ncbi request reprint The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins
    Jorn Kalinowski
    Institut für Genomforschung, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
    J Biotechnol 104:5-25. 2003
    ..As an example for biotechnological application the complete genome sequence was used to reconstruct the metabolic flow of carbon into a number of industrially important products derived from the amino acid L-aspartate...
  41. doi request reprint Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids
    Andreas Tauch
    Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
    J Biotechnol 136:22-30. 2008
    ..A complete beta-oxidation pathway involved in the degradation of fatty acids is present in the genome. Evaluation of the genomic data indicated that lipophilism is the dominant feature involved in pathogenicity of C. kroppenstedtii...
  42. doi request reprint The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing
    Andreas Tauch
    Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
    J Biotechnol 136:11-21. 2008
    ..The complete genome sequence of C. urealyticum revealed a detailed picture of the lifestyle of this opportunistic human pathogen...
  43. pmc Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora
    Andreas Tauch
    Institut für Genomforschung, Centrum für Biotechnologie, Universitat Bielefeld, Universitatsstrasse 25, D 33615 Bielefeld, Germany
    J Bacteriol 187:4671-82. 2005
    ..The predicted virulence factors of C. jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by damaging the host tissue...
  44. doi request reprint New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics
    Jörg Toepel
    Algae Biotechnology and Bioenergy Group, Department of Biology Center for Biotechnology, Bielefeld University, Bielefeld, Germany
    Plant Biotechnol J 11:717-33. 2013
    ..RNA-seq additionally allowed a detailed time-dependent study of gene expression and determination of new genes involved in the hydrogen production process. ..
  45. ncbi request reprint An evaluation framework for statistical tests on microarray data
    Michael Dondrup
    Center for Biotechnology, Bielefeld University, Bielefeld, Germany
    J Biotechnol 140:18-26. 2009
    ..Specifically, we report that for four replicates all methods reach a high to very high correlation with our reference standard...
  46. doi request reprint Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora
    Fabio Rezzonico
    Agroscope Changins Wädenswil ACW, Plant Protection Division, Swiss National Competence Centre for Fire Blight, CH 8820 Wadenswil, Switzerland
    Mol Plant Pathol 13:975-84. 2012
    ..The LPS biosynthesis gene cluster may thus be used as a molecular marker to distinguish between Rubus- and Spiraeoideae-infecting strains of E. amylovora using primers designed in this study...
  47. pmc A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study
    Stefan P Albaum
    Computational Genomics, Center for Biotechnology CeBiTec, Bielefeld University, Germany
    Proteome Sci 9:30. 2011
    ..abstract:..
  48. pmc Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii
    Jörg Toepel
    Algae Biotechnology and Bioenergy, Dept, of Biology, Center for Biotechnology CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
    BMC Genomics 12:579. 2011
    ..Based on the completed annotation of Chlamydomonas reinhardtii a new microarray on an Agilent platform was designed using an extended JGI 3.1 genome data set which included 15000 transcript models...
  49. pmc MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula
    Kolja Henckel
    Bioinformatics of Signaling Networks, Center for Biotechnology, Bielefeld University, Germany
    BMC Res Notes 3:262. 2010
    ..Under these circumstances, the challenge arises to combine results derived from the different expression profiling strategies, with the goal to uncover novel information on the basis of the integrated datasets...
  50. ncbi request reprint Complete genome sequence of the myxobacterium Sorangium cellulosum
    Susanne Schneiker
    Department of Genetics, Bielefeld University, PO Box 100131, D 33501 Bielefeld, Germany
    Nat Biotechnol 25:1281-9. 2007
    ..Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry...
  51. ncbi request reprint BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
    Daniela Bartels
    Universitat Bielefeld, Center for Biotechnology CeBiTec D 33594 Bielefeld, Germany
    Bioinformatics 21:853-9. 2005
    ..The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries...
  52. ncbi request reprint Antibiotic multiresistance plasmid pRSB101 isolated from a wastewater treatment plant is related to plasmids residing in phytopathogenic bacteria and carries eight different resistance determinants including a multidrug transport system
    Rafael Szczepanowski
    Fakultat fur Biologie, Lehrstuhl fur Genetik, Universitat Bielefeld, Postfach 100131, D 33501 Bielefeld, Germany
    Microbiology 150:3613-30. 2004
    ....
  53. ncbi request reprint A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective
    Snjezana Rendulic
    Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Science 303:689-92. 2004
    ..A plethora of paralogous gene families coding for enzymes, such as hydrolases and transporters, are used throughout the life cycle of B. bacteriovorus for prey entry, prey killing, and the uptake of complex molecules...
  54. pmc The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP)
    Joakim Westberg
    Department of Biotechnology, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    Genome Res 14:221-7. 2004
    ....
  55. pmc The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    Ross Overbeek
    Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA
    Nucleic Acids Res 33:5691-702. 2005
    ..The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms...
  56. pmc Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence
    Frank Thieme
    Martin Luther Universitat, Institut fur Genetik, Weinbergweg 10, D 06120 Halle Saale, Germany
    J Bacteriol 187:7254-66. 2005
    ..Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides...
  57. ncbi request reprint Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis
    Susanne Schneiker
    Lehrstuhl fur Genetik, Fakultat fur Biologie, Universitat Bielefeld, D 33594 Bielefeld, Germany
    Nat Biotechnol 24:997-1004. 2006
    ..borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills...
  58. doi request reprint Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11
    Michael Stiens
    Fakultat fur Biologie, Lehrstuhl fur Genetik, Universitat Bielefeld, Postfach 100131, D 33501 Bielefeld, Germany
    J Biotechnol 136:31-7. 2008
    ..iii) S. meliloti SM11 megaplasmid pSymB lacks a complete cell surface carbohydrate synthesis gene cluster. (iv) Several genes that are absent in the SM11 genome could be assigned to insertion sequences and transposons...
  59. pmc Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis
    Christoph Schoen
    Institute for Hygiene and Microbiology, University of Wurzburg, Josef Schneider Strasse 2, 97080 Wurzburg, Germany
    Proc Natl Acad Sci U S A 105:3473-8. 2008
    ..meningitidis has emerged as an unencapsulated human commensal from a common ancestor with Neisseria gonorrhoeae and Neisseria lactamica and consecutively acquired the genes responsible for capsule synthesis via horizontal gene transfer...
  60. pmc The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity
    Karl Heinz Gartemann
    Lehrstuhl für Gentechnologie Mikrobiologie, Universitat Bielefeld, D 33501 Bielefeld, Germany
    J Bacteriol 190:2138-49. 2008
    ..michiganensis subsp. michiganensis dependent on reduced sulfur compounds for growth, is probably the reason for the poor survival of C. michiganensis subsp. michiganensis in soil...
  61. pmc The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae
    Roy Gross
    Chair of Microbiology, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    BMC Genomics 9:449. 2008
    ..Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described...
  62. pmc Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363
    Udo Wegmann
    Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    J Bacteriol 189:3256-70. 2007
    ..The availability of the L. lactis MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research...
  63. ncbi request reprint The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups
    Martin Iain Bahl
    Department of Microbiology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen K, Denmark
    Plasmid 58:31-43. 2007
    ....
  64. ncbi request reprint Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72
    Andrea Krause
    Laboratory of General Microbiology, University of Bremen, PO Box 330440, D 28334 Bremen, Germany
    Nat Biotechnol 24:1385-91. 2006
    ..The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment...
  65. pmc Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes
    Torsten Hain
    Institute for Medical Microbiology, Justus Liebig University, Frankfurter Strasse 107, D 35392 Giessen, Germany
    J Bacteriol 188:7405-15. 2006
    ..The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp...
  66. doi request reprint The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis
    Frank Jörg Vorhölter
    Universitat Bielefeld, Biologie VI Genetik, Universitatsstr 25, D 33615 Bielefeld, Germany
    J Biotechnol 134:33-45. 2008
    ..The updated genome annotation data allowed reconsidering and refining the mechanistic model for xanthan biosynthesis...
  67. ncbi request reprint Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara
    Christine Meisinger-Henschel
    Bavarian Nordic GmbH, Fraunhoferstrasse 13, D 82152 Martinsried, Germany
    J Gen Virol 88:3249-59. 2007
    ..Thus, detailed knowledge of the CVA genomic sequence is a prerequisite to further dissect the genetic basis of the MVA host range phenotype as well as the particular immunological properties of MVA...